UKBioPick

The UKBioPick allows extraction of interested UK Biobank (UKBB) phenotypes from tab-delimited phenotypic file (ukbxxxx.tab).

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Requirements

• Bash
• Perl
• UKBB phenotypic tab-delimited file (ukbxxxx.tab)
• Create a tab-separated file contains Field ID (column1) and Field (column2) (see example here. You can select Field ID and Field for each UKBB phenotypes in the UKBB data dictionary Data_Dictionary_Showcase.

Usage

You must supply at least [4] arguments when running a UKBioPick!

Arguments	Description
arg1	UKBB phenotypic tab file (ukbxxxx.tab)
arg2	Field ID and Field file
arg3	Path to output directory
arg4	Project name

You can run UKBioPick using the following command:

bash run_UKBioPick.sh [arg1:UKBB_phenotypics_tab_file] [arg2:field_ID_file] [arg3:output_directory] [arg4:project_name]

Outputs

UKBioPick generates 2 output files:

• <project_name>_ ukb_selected_phenotypes.tab: contains extracted phenotypes in tab-delimited file (similar to original tab file "ukbxxxx.tab").
• <project_name>_ ukb_selected_phenotypes.info: shows information about phenotypes availability in the ukbxxxx.tab file, number of measure for each phenotype, and column location on both original and extracted tab file. Click here to see example

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Available UKBB phenotypes at dhl_ec (UMC Utrecht)

• The lates version of UKBB phenotypes file (ukbxxxx.tab) in the HPC is ukb44641.tab.
• You can find the ukb44641.tab in this path.

/hpc/dhl_ec/data/ukbiobank/phenotypic/ukb44641.tab

Slides

These slides have information about UKBB phenotypes at dhl_ec. Click here to view slides.

Contact

If you have any suggestions for improvement, discover bugs, etc. please create an issues. For all other questions, please refer to the last author:

Abdulrahman Alasiri | a.i.alasiri [at] umcutrecht.nl

License and copyright

MIT License

Copyright (c) 2021-2031 Abdulrahman Alasiri